:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cnvpytor' .. highlight: bash cnvpytor ======== .. conda:recipe:: cnvpytor :replaces_section_title: :noindex: Python extension of CNVnator :homepage: https://github.com/abyzovlab/CNVpytor :license: MIT / MIT :recipe: /`cnvpytor `_/`meta.yaml `_ .. conda:package:: cnvpytor |downloads_cnvpytor| |docker_cnvpytor| :versions: ``1.3.1-1``,  ``1.3.1-0``,  ``1.2.1-0``,  ``1.0-2``,  ``1.0-1``,  ``1.0-0``,  ``1.0b3-1``,  ``1.0b3-0`` :depends chardet: :depends h5py: ``>=2.9`` :depends matplotlib-base: ``>=2.2`` :depends numpy: ``>=1.16`` :depends pathlib: ``>=1.0`` :depends pysam: ``>=0.15`` :depends python: ``>=3.6`` :depends requests: ``>=2.0`` :depends scipy: ``>=1.1`` :depends xlsxwriter: ``>=1.3`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install cnvpytor and update with:: mamba update cnvpytor To create a new environment, run:: mamba create --name myenvname cnvpytor with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/cnvpytor: (see `cnvpytor/tags`_ for valid values for ````) .. |downloads_cnvpytor| image:: https://img.shields.io/conda/dn/bioconda/cnvpytor.svg?style=flat :target: https://anaconda.org/bioconda/cnvpytor :alt: (downloads) .. |docker_cnvpytor| image:: https://quay.io/repository/biocontainers/cnvpytor/status :target: https://quay.io/repository/biocontainers/cnvpytor .. _`cnvpytor/tags`: https://quay.io/repository/biocontainers/cnvpytor?tab=tags .. raw:: html Notes ----- The package comes with downloaded reference data\, such that \`cnvpytor \-download\` can be omitted. Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/cnvpytor/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cnvpytor/README.html